Mercurial > repos > iuc > imagej2_shadows
diff imagej2_bunwarpj_elastic_transform_jython_script.py @ 2:ef4de385bbde draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
| author | iuc |
|---|---|
| date | Fri, 22 Jul 2016 23:22:12 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_bunwarpj_elastic_transform_jython_script.py Fri Jul 22 23:22:12 2016 -0400 @@ -0,0 +1,16 @@ +import sys +import jython_utils +from ij import IJ + +# Fiji Jython interpreter implements Python 2.5 which does not +# provide support for argparse. + +source_tiff_path = sys.argv[ -3 ] +source_datatype = sys.argv[ -2 ] +source_path = sys.argv[ -1 ] + +# Save the Registered Source Image. +registered_source_image = IJ.openImage( source_tiff_path ) +if source_datatype == 'tiff': + registered_source_image = jython_utils.convert_before_saving_as_tiff( registered_source_image ) +IJ.saveAs( registered_source_image, source_datatype, source_path )